Evolutionary consequences of natural hybridization between two species vary drastically depending on spatial, genetic and ecological circumstances. Uncovering the outcomes of this process is facilitated by using multiple approaches ranging from molecular markers to niche modeling. In this work, the complex nature of the Iberian natural hybrid Narcissus ×perezlarae is clarified. Four organellar and one nuclear sequence markers reveal that it actually consists of two different hybrid taxa, Narcissus ×perezlarae (N. cavanillesii × N. miniatus) and N. ×alentejanus (N. cavanillesii × N. serotinus), the mother species being predominantly N. cavanillesii. This framework is also supported by chromosome counts, genome size and experimental crosses. Throughout their ranges, different situations are found with regard to hybrid occurrence: sympatric populations without hybrids, sympatric populations where hybrids occur and populations where hybrids occur but their parents are lacking (‘orphan hybrid populations’). Also, we analyzed the causes for the orphan hybrid populations of N ×perezlarae in eastern Spain, where the closest populations of the mother parent N. cavanillesii lie 450 km apart. Ecological niche modeling reveals similar requirements for N. ×perezlarae and their parental species suggesting niche competition among them. The markedly higher ability to propagate asexually by bulbs in N. ×perezlarae as compared to their parents and the low reproductive barriers to fertilization by foreign pollen in N. cavanillesii suggest that the latter has been extirpated as a result of hybridization via demographic swamping and competition.